编辑“︁古菌”︁（章节）

== 歷史 ==
=== 新域的诞生 ===
[[File:Aerial image of Grand Prismatic Spring (view from the south).jpg|thumb|right|250px|古菌最早是在一些极端环境，如火山[[温泉]]中发现的。图为[[黄石国家公园]]的[[大棱镜温泉]]。]]

在20世纪的大部分时间里，原核生物因其[[生物化学|生化]]、[[生物形態學|形态]]和[[代谢]]上的一致性被视为分类上的单组生物。在这一时期，微生物学家试图根据其形状、[[细胞壁]]结构以及所消耗的物质来对微生物进行分类<ref>{{Cite journal |last=Staley |first=James T |date=2006-11-29 |title=The bacterial species dilemma and the genomic–phylogenetic species concept |url=https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1914 |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |language=en |volume=361 |issue=1475 |doi=10.1098/rstb.2006.1914 |issn=0962-8436 |pmc=1857736 |pmid=17062409 |access-date=2022-10-13 |archive-date=2022-09-30 |archive-url=https://web.archive.org/web/20220930201102/https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1914 |dead-url=no }}</ref>。然而，在1965年有一种新方法被提出<ref>{{Cite journal |last=Zuckerkandl |first=Emile |last2=Pauling |first2=Linus |date=1965-03-01 |title=Molecules as documents of evolutionary history |url=https://www.sciencedirect.com/science/article/pii/0022519365900834 |journal=Journal of Theoretical Biology |language=en |volume=8 |issue=2 |doi=10.1016/0022-5193(65)90083-4 |issn=0022-5193 |pmid=5876245 |access-date=2022-10-13 |archive-date=2018-12-08 |archive-url=https://web.archive.org/web/20181208131131/https://www.sciencedirect.com/science/article/pii/0022519365900834 |dead-url=no }}</ref>，即使用生物体的[[基因]]序列来搞清这些生物是如何相关联的。这种方法称为[[系统发生学]]（phylogenetics），是今天生物分类所使用的主要方法。
[[Image:Morning-Glory Hotspring.jpg|thumb|left|250px|古菌賦予溫泉（例如牽牛花溫泉）顏色。]]

「古细菌」这个概念第一次出现是在1977年，由[[卡尔·乌斯]]和[[乔治·福克斯 (生物学家)|乔治·福克斯]]提出的，原因是它們在[[16S 核糖体RNA]]的[[系統發生樹]]上和其牠原核生物的區別<ref>{{Cite journal |last=Woese |first=Carl R. |last2=Fox |first2=George E. |date=1977-11 |title=Phylogenetic structure of the prokaryotic domain: The primary kingdoms |url=https://pnas.org/doi/full/10.1073/pnas.74.11.5088 |journal=Proceedings of the National Academy of Sciences |language=en |volume=74 |issue=11 |bibcode=1977PNAS...74.5088W |doi=10.1073/pnas.74.11.5088 |issn=0027-8424 |access-date=2022-10-13 |archive-date=2022-10-13 |archive-url=https://web.archive.org/web/20221013155155/https://www.pnas.org/doi/full/10.1073/pnas.74.11.5088 |dead-url=no }}</ref>。這兩組原核生物起初被定為古細菌和真細菌兩個[[界 (生物)|界]]或[[亞界]]（当时乌斯与福克斯更倾向于用「总界」一词）。后来[[卡尔·乌斯|乌斯]]認為它們是兩支根本不同的生物，於是在1990年重新命名其為古菌和細菌<ref name="Woese">{{Cite journal |last=Woese |first=C R |last2=Kandler |first2=O |last3=Wheelis |first3=M L |date=1990-06 |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. |url=https://pnas.org/doi/full/10.1073/pnas.87.12.4576 |journal=Proceedings of the National Academy of Sciences |language=en |volume=87 |issue=12 |bibcode=1990PNAS...87.4576W |doi=10.1073/pnas.87.12.4576 |issn=0027-8424 |pmc=54159 |pmid=2112744 |access-date=2022-10-13 |archive-date=2023-09-16 |archive-url=https://web.archive.org/web/20230916192227/https://www.pnas.org/doi/abs/10.1073/pnas.87.12.4576 |dead-url=no }}</ref>，并将這兩支和真核生物划为[[域 (生物)|域]]这一新建立的[[分類階級|分类阶元]]，一起構成了生物的[[三域系統]]。

起初只有一些[[产甲烷菌]]属于这个新域，这些古菌以一些极端环境为栖息地，比如[[温泉]]和[[咸水湖|盐湖]]。到20世纪末，微生物学家意识到古菌是一个庞大而多元化的群体，不只局限于极端环境，而是广泛存在于自然界中，如土壤和海洋里<ref name="DeLong">{{Cite journal |last=DeLong |first=Edward F |date=1998-12-01 |title=Everything in moderation: Archaea as ‘non-extremophiles’ |url=https://www.sciencedirect.com/science/article/pii/S0959437X98800324 |journal=Current Opinion in Genetics & Development |language=en |volume=8 |issue=6 |doi=10.1016/S0959-437X(98)80032-4 |issn=0959-437X |pmid=9914204}}</ref>。由于[[聚合酶链式反应]]（PCR）被大量用于探测采样土壤或水中的[[原核生物]]的[[核酸]]，古菌的重要性和独特性得到新的重视。PCR方法可以不经{{Link-en|细菌培养|microbiological culture}}而直接探测和鉴别微生物<ref>{{Cite journal |last=Theron |first=J. |last2=Cloete |first2=T. E. |date=2000-01 |title=Molecular Techniques for Determining Microbial Diversity and Community Structure in Natural Environments |url=http://www.tandfonline.com/doi/full/10.1080/10408410091154174 |journal=Critical Reviews in Microbiology |language=en |volume=26 |issue=1 |doi=10.1080/10408410091154174 |issn=1040-841X |pmid=10782339}}</ref><ref>{{Cite journal |last=Schmidt |first=Thomas M. |date=2006-09 |title=The maturing of microbial ecology |url=https://pubmed.ncbi.nlm.nih.gov/17061212/ |journal=International Microbiology: The Official Journal of the Spanish Society for Microbiology |volume=9 |issue=3 |issn=1139-6709 |pmid=17061212 |access-date=2022-10-13 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014180727/https://pubmed.ncbi.nlm.nih.gov/17061212/ |dead-url=no }}</ref>。

=== 现行分类 ===
{{See also|生物分類法|系統分類學}}

[[File:Rio tinto river CarolStoker NASA Ames Research Center.jpg|thumb|200px|left|{{tsl|en|archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}：2006年在西班牙[[廷托河]]的{{le|矿渣酸性废水|acid mine drainage}}中发现的古菌新类群]]
古菌和原核生物的分类一般是一个快速发展并充满争议的领域。现行的分类体系旨在将古菌组织成具有共同结构特征和共同祖先的生物群<ref name="Gevers">{{Cite journal |last=Gevers |first=Dirk |last2=Dawyndt |first2=Peter |last3=Vandamme |first3=Peter |last4=Willems |first4=Anne |last5=Vancanneyt |first5=Marc |last6=Swings |first6=Jean |last7=De Vos |first7=Paul |date=2006-11-29 |title=Stepping stones towards a new prokaryotic taxonomy |url=https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1915 |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=361 |issue=1475 |doi=10.1098/rstb.2006.1915 |issn=0962-8436 |pmc=1764938 |pmid=17062410 |access-date=2022-10-13 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017010347/https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1915 |dead-url=no }}</ref>。这些分类很大程度上依赖于使用[[核糖体RNA]]基因序列来揭示生物之间的关系（[[分子系统发生学]]）<ref name="Robertson">{{Cite journal |last=Robertson |first=Charles E |last2=Harris |first2=J Kirk |last3=Spear |first3=John R |last4=Pace |first4=Norman R |date=2005-12-01 |title=Phylogenetic diversity and ecology of environmental Archaea |url=https://www.sciencedirect.com/science/article/pii/S1369527405001591 |journal=Current Opinion in Microbiology |series=Growth development / edited by John N Reeve and Ruth A Schmitz |language=en |volume=8 |issue=6 |doi=10.1016/j.mib.2005.10.003 |issn=1369-5274 |pmid=16236543}}</ref>。目前大部分可纯化培养的并研究清楚的古菌都可以划为两个主要的[[门 (生物)|门]]：[[泉古菌门]]和[[廣古菌门]]。其它的门类还在初步创立阶段，比如2002年由[[卡尔·施泰特尔]]發現的奇特的物種{{tsl|en|Nanoarchaeum equitans|骑行纳古菌}}而建立的[[納古菌门]]<ref>{{Cite journal |last=Huber |first=Harald |last2=Hohn |first2=Michael J. |last3=Rachel |first3=Reinhard |last4=Fuchs |first4=Tanja |last5=Wimmer |first5=Verena C. |last6=Stetter |first6=Karl O. |date=2002-05-02 |title=A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont |url=https://www.nature.com/articles/417063a |journal=Nature |language=en |volume=417 |issue=6884 |bibcode=2002Natur.417...63H |doi=10.1038/417063a |issn=0028-0836 |pmid=11986665 |access-date=2022-10-13 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018043353/https://www.nature.com/articles/417063a |dead-url=no }}</ref>。还有1994年Barns等建议建立的一个新门[[初古菌门]]包括一小群不寻常的嗜热品种，但这个门与泉古菌门演化关系密切<ref>{{Cite journal |last=Barns |first=S M |last2=Delwiche |first2=C F |last3=Palmer |first3=J D |last4=Pace |first4=N R |date=1996-08-20 |title=Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. |url=https://pnas.org/doi/full/10.1073/pnas.93.17.9188 |journal=Proceedings of the National Academy of Sciences |language=en |volume=93 |issue=17 |bibcode=1996PNAS...93.9188B |doi=10.1073/pnas.93.17.9188 |issn=0027-8424 |pmc=38617 |pmid=8799176}}</ref><ref>{{Cite journal |last=Elkins |first=James G. |last2=Podar |first2=Mircea |last3=Graham |first3=David E. |last4=Makarova |first4=Kira S. |last5=Wolf |first5=Yuri |last6=Randau |first6=Lennart |last7=Hedlund |first7=Brian P. |last8=Brochier-Armanet |first8=Céline |last9=Kunin |first9=Victor |last10=Anderson |first10=Iain |last11=Lapidus |first11=Alla |date=2008-06-10 |title=A korarchaeal genome reveals insights into the evolution of the Archaea |url=https://pnas.org/doi/full/10.1073/pnas.0801980105 |journal=Proceedings of the National Academy of Sciences |language=en |volume=105 |issue=23 |bibcode=2008PNAS..105.8102E |doi=10.1073/pnas.0801980105 |issn=0027-8424 |pmc=2430366 |pmid=18535141 |access-date=2022-10-13 |archive-date=2022-11-08 |archive-url=https://web.archive.org/web/20221108154907/https://www.pnas.org/doi/full/10.1073/pnas.0801980105 |dead-url=no }}</ref>。其它最近探别出来的古菌与已知古菌门类关系较远，如2006年发现的環境樣品{{tsl|en|Archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}<ref>{{Cite journal |last=Baker |first=Brett J. |last2=Tyson |first2=Gene W. |last3=Webb |first3=Richard I. |last4=Flanagan |first4=Judith |last5=Hugenholtz |first5=Philip |last6=Allen |first6=Eric E. |last7=Banfield |first7=Jillian F. |date=2006-12-22 |title=Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis |url=https://www.science.org/doi/10.1126/science.1132690 |journal=Science |language=en |volume=314 |issue=5807 |bibcode=2006Sci...314.1933B |doi=10.1126/science.1132690 |issn=0036-8075 |pmid=17185602 |access-date=2022-10-13 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014171212/https://www.science.org/doi/10.1126/science.1132690 |dead-url=no }}</ref><ref name="Baker BJ, Comolli LR, Dick GJ, et al. 8806–11">{{cite journal |author=Baker BJ |author2=Comolli LR |author3=Dick GJ |display-authors=etal|date=May 2010 |title=Enigmatic, ultrasmall, uncultivated Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=107 |issue=19 |pages=8806–11 |bibcode=2010PNAS..107.8806B |doi=10.1073/pnas.0914470107 |pmc=2889320 |pmid=20421484}}</ref>。{{tsl|en|Archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}是已知的生命體中最小的生命體<ref name="Baker BJ, Comolli LR, Dick GJ, et al. 8806–11" />。

一个超门（superphylum）分类-TACK（又稱[[變形古菌界]]），已经被提出，包括{{le|奇古菌门|Thaumarchaeota}}，{{le|曙古菌門|Aigarchaeota}}，[[泉古菌門]]和[[初古菌門]]<ref name="Guy2011">{{Cite journal |last=Guy |first=Lionel |last2=Ettema |first2=Thijs J. G. |date=2011-12-01 |title=The archaeal ‘TACK’ superphylum and the origin of eukaryotes |url=https://www.cell.com/trends/microbiology/abstract/S0966-842X(11)00174-0 |journal=Trends in Microbiology |language=en |volume=19 |issue=12 |doi=10.1016/j.tim.2011.09.002 |issn=0966-842X |pmid=22018741 |access-date=2022-10-13 |archive-date=2013-10-16 |archive-url=https://web.archive.org/web/20131016220820/http://www.cell.com/trends/microbiology/abstract/S0966-842X(11)00174-0 |dead-url=no }}</ref>。这个超门可能与真核生物的起源有关。最近，[[阿斯加德古菌超门]]被命名，并被提议与真核生物的起源和一个TACK姊妹组织更紧密相关<ref>{{Cite journal |last=Zaremba-Niedzwiedzka |first=Katarzyna |last2=Caceres |first2=Eva F. |last3=Saw |first3=Jimmy H. |last4=Bäckström |first4=Disa |last5=Juzokaite |first5=Lina |last6=Vancaester |first6=Emmelien |last7=Seitz |first7=Kiley W. |last8=Anantharaman |first8=Karthik |last9=Starnawski |first9=Piotr |last10=Kjeldsen |first10=Kasper U. |last11=Stott |first11=Matthew B. |date=2017-01-19 |title=Asgard archaea illuminate the origin of eukaryotic cellular complexity |url=https://www.nature.com/articles/nature21031 |journal=Nature |language=en |volume=541 |issue=7637 |doi=10.1038/nature21031 |issn=0028-0836 |access-date=2022-10-13 |archive-date=2022-12-03 |archive-url=https://web.archive.org/web/20221203044937/https://www.nature.com/articles/nature21031 |dead-url=no }}</ref>。